many workshops use thicker gaskets and get away with it, many very high power engines also feature these. I would say over 95% of the time thicker gaskets are used when people want to up the boost. This will lead to a greater top end power and people liking it because for the aim it worked. Its cheap and hence many people do it, however that doesnt mean its not flawed. If however one engine with that method and another with a matched quench zone but a deeper dish was compared then the real story would be shown. Well quenched chambers are known for very high detonation resistance. Although I do admit in the case of the a blacktop it would not have that much of a change due to the fact the almost complete lack of a convention quench zone and the replacement of it with a contoured piston shape.
I tottaly agree with you on the service question, given that a head was skimmed a fair bit I would very likely just go the gasket as well. This particular case though just needs the silvertop pistons and might even be cheaper than the thicker head gasket.